David Posada

Unraveling the Phylogenetic Signal of Gene Expression from Single-cell RNA-seq Data Abstract. Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of phenotypic heterogeneity. Although the predominant focus of scRNA-seq

🔬 Our new study in GPB shows that we can recover cell phylogenies from scRNA-seq data and distinguish tumor vs. normal lineages.

🧬 Most expression variation is transcriptionally plastic, but cell‑cycle genes showed a strong phylogenetic signal in one patient.

👉 academic.oup.com/gpb/advance-...

🔥🔥🔥💥💥💥🌶️🌶️🌶️ Hottest new lab in town, led by the exceptional @calumgabbutt.bsky.social, is recruiting it's first #PhD student. If you love #maths and somatic #evolution it could be your dream come true! 🌶️🌶️🌶️💥💥💥🔥🔥🔥

Cancer evolution and multi-omic profile of relapsed colorectal liver metastases after treatment - Genome Medicine Genome Medicine - Recurrence following resection of colorectal cancer liver metastases remains a major obstacle to prolonged patient survival, often resulting in treatment-refractory disease with...

🧬 New in Genome Medicine! Deep genomic analysis of relapsed colorectal cancer liver metastases reveals patient-specific evolutionary trajectories and multiple routes to recurrence.

link.springer.com/article/10.1...

🤝 Nice collaboration with @soulafa.bsky.social & colleagues

Postdoctoral Training Fellow - Genomics and Evolutionary Dynimcs in Sutton | The Institute of Cancer Research View details and apply for this Postdoctoral Training Fellow - Genomics and Evolutionary Dynimcs vacancy in Sutton. Salary: Dependent on relevant Postdoctoral experience. Durati...

Open postdoc position in our lab @icr.ac.uk to develop a cfDNA test for #early detection of colorectal #cancer in inflammatory bowel disease #IBD:
jobs.icr.ac.uk/vacancies/14...

It's bench-to-bedside research, translating biology of pre-cancer evolution.

Funded by @bowelcanceruk.bsky.social

Single-cell phylodynamics reveal rapid late-stage colorectal cancer expansions Single-cell whole-genome sequencing of 335 cells from seven colorectal cancers, coupled with Bayesian phylodynamic modeling, revealed tumors often originate decades before diagnosis, remain indolent, ...

🧬 New preprint out on bioRxiv!

Using single-cell WGS and Bayesian phylodynamics, we show that some CRC tumors arise decades before diagnosis, remain indolent, then expand rapidly in the last ~2 years.

📄 doi.org/10.1101/2025...

🙏 Huge thanks to all co-authors

Data Scientist in Sutton | The Institute of Cancer Research View details and apply for this Data Scientist vacancy in Sutton. Salary : Salary range £39,805 to £53,500 (Dependent on experience ) Reporting to: Professor Trevor Gra...

Calling cancer data scientists! 📊 💽 🧮
We have a number of open positions in our core facility @icr.ac.uk These are bioinformatician staff scientist like roles to work on exciting single cell, spatial & other genomics data from across our Institute. A PhD is required. jobs.icr.ac.uk/vacancies/13...

Become part of a Marie Skłodowska-Curie Doctoral Network a prestigious EU initiative offering world-class research training, international experience, and strong career prospects for early-stage researchers.
It’s more than a PhD:it’s a launchpad for your research career!
Apply now: www.evomg-dn.eu

We are hiring a postdoc to profile the evolvability of tumors in longitudinal samples from three clinical trials as part of the ARPA-H ADAPT program. This is essentially an evolutionary bioinformatics position. If you are interested, please apply here ASAP apply.interfolio.com/172521

We have two fantastically well-funded #PhD studentships available through the @evomg-dn.bsky.social #EU doctoral network (led by brilliant @mirimiam.bsky.social, @crg.eu). These enable students to move to the UK and come and work with us @icr.ac.uk to exploit #cancer #evolution for patient benefit.

The second is about potential fitness costs of cancer drug resistance, and how we might exploit them using approaches like adaptive therapy. (building on our work with @mlockley.bsky.social in ovarian cancer: aacrjournals.org/cancerres/ar...). Description here: www.icr.ac.uk/study-and-ca...

📢 EvoMG-DN PhD applications are now open!
Join our EU-funded MSCA network and explore evolution, ageing, and disease.
👉 www.evomg-dn.eu

📅 Apply by 30 November 2025

#PhD #DoctoralTraining #MSCA #HorizonEurope #Genomics #EvolutionaryBiology #BiomedicalResearch#EarlyCareerResearchers

David Posada, CINBIO, U Vigo

And the last session of the meeting was Session 5: Cancer.

The first speaker was David Posada ( @davidposada.bsky.social ), from the Universidade de Vigo and @cinbio.bsky.social, who showed us how somatic phylogenetics can provide fundamental insights into the evolutionary dynamics of cancer.

📢 PhD position at the Posada Lab!

🚀 Join us at the University of Vigo to track how tumor cells evolve, adapt, and survive using cutting-edge single-cell DNA/RNA tech. 4-year PhD, €134K total funding—apply by Nov 3, 2025.

👉 dposada.webs.uvigo.es/2025/10/07/p...

Genomic diversity and BCL9L mutational status in circulating tumor cells predict overall survival in metastatic colorectal cancer - Cellular Oncology Background Metastatic colorectal cancer (mCRC) remains a major cause of cancer-related mortality, but few noninvasive biomarkers exist to track disease progression or inform treatment strategies. Circulating tumor cells (CTCs) offer a minimally invasive source of tumor material, yet the prognostic significance of their genomic diversity remains unclear. Methods We conducted whole-exome sequencing of CTC pools from 29 mCRC patients to characterize their mutational landscape and assess associations with overall survival. Results Our analysis revealed substantial variation in mutational burden among patients, with all CTC pools harboring non-silent mutations in key CRC driver genes. Higher genomic diversity in CTC pools was significantly associated with reduced overall survival. Additionally, non-silent mutations in BCL9L emerged as a strong predictor of patient survival. Conclusion Genomic diversity and BCL9L mutational status in CTC pools emerged as strong predictors of survival in mCRC, underscoring the potential of CTC genomic profiling as a minimally invasive and clinically relevant prognostic tool in mCRC.

🚨Our new study in Cellular Oncology🚨 shows high CTC genomic diversity & BCL9L mutations predict worse survival in metastatic colorectal cancer—supporting liquid biopsy for prognosis. 🎯🧬

Thanks to all co-authors!

doi.org/10.1007/s134...

It was not something I heard, but something I saw: hope in their eyes

It was a pleasure to join @aecc_es in Pontevedra for the World Cancer Research Day — talking with and listening to patients about the power of science and hope. Without research, there’s no cure. 💚 #ScienceIsHope"

Big congrats Monica! so well-deserved! 👏

Fluctuating DNA methylation tracks cancer evolution at clinical scale - Nature Cancer evolutionary dynamics are quantitatively inferred using a method, EVOFLUx, applied to fluctuating DNA methylation.

Studying cancer evolution needs multi-region or single cell seq for phylogenetics, right? Amazingly (I think!) we found single-sample bulk methylation suffices, via analysis of "fluctuating methylation". In @nature.com today led by brilliant @calumgabbutt.bsky.social www.nature.com/articles/s41...

🤚

Very nice work @trevorgraham.bsky.social and colleagues!! 👏

🚀 Excited to share our latest collaboration with Ewa Szczurek’s lab (@ewaszczurek.bsky.social) et al. in Genome Biology!

🧬 DelSIEVE: single-cell phylogeny from SNVs & indels 🧬

👉 rdcu.be/eCnL3

Big thanks to Senbai and Ewa for leading this project, and to all collaborators who made it possible! 🙌

🎉 Last week, Nair successfully defended her Ph.D thesis on the genomic heterogeneity of circulating tumor cells and their role in metastasis! Her research sheds light on how cancer spreads. Huge congratulations to Nair on this outstanding achievement! 👏🧬

Intraline genomic heterogeneity of the triple-negative breast cancer MDA-MB-231-luc-GFP cell line Cancer cell lines are valuable models for studying tumor biology, yet their genomic evolution during culture can compromise experimental reproducibility. We conducted a detailed genomic analysis of th...

Intraline genomic heterogeneity of the TNBC MDA-MB-231-luc-GFP cell line www.csbj.org/article/S200...

International importance and spread of SARS-CoV-2 variants Alpha, Delta, and Omicron BA.1 into Spain Communications Medicine - Gallego García et al. trace the entry and spread of SARS-CoV-2 Alpha, Delta, and Omicron BA.1 into Spain. The main route of entry is via France, the United Kingdom,...

🦠 New paper out in Communications Medicine!

🌍🔬 We tracked the global spread and introductions of SARS-CoV-2 variants Alpha, Delta, and Omicron BA.1 into Spain.

Great collaboration with @lemeylab.bsky.social @guybaele.bsky.social @msuchard.bsky.social and others

📖 rdcu.be/eoG7x

🚨 New paper out in Cell Reports Methods! 🧬✨
After a long, long journey, we're thrilled to share our deep-dive into six single-cell whole-genome amplification (scWGA) methods.

🔍 TL;DR: no one-size-fits-all

Huge congrats to the whole team!

📝 doi.org/10.1016/j.cr...

Steve Kerr wore a Harvard basketball shirt after the Warriors’ win tonight: “Yes, this is me supporting Harvard. Way to go. Way to stand up to the bully.”

"Many, and perhaps most, members of our academic community do not understand [the benefits of publishing] in society-based journals ... compared with for-profit journals from companies like Springer Nature, Frontiers, Wiley, and Elsevier." 🧪

academic.oup.com/mbe/article/...

Our #Cancer #Evolution summer school runs again 30 June-3 July at the beautiful Genome Campus in Hinxton, UK sponsored by @wellcometrust.bsky.social

Ideal for starters in the field; this year's focus is on using genomic data for cancer evo research.

Brilliant & inspiring faculty! bit.ly/40nLdDD

We have two open positions for #computationalbiologists to work on:
1. Early cancer initiation following our work in #NatureCancer (Ref 5028)
2. Response to cancer immunotherapy following our work in #CancerCell (Ref 5073)
To apply use the provided reference numbers: www.qmul.ac.uk/jobs/vacanci...

🎓 Como School on Cancer Evolution (CSCE 2025) for cutting-edge discussions on cancer biology, computational sciences, AI, and more! 🧬🌟 May 27-30, 2025, Villa del Grumello, Como, Italy 🇮🇹. Present your research & network with pioneers in the field. Register at: csce.lakecomoschool.org/registration/